GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Desulforamulus ruminis DSM 2154

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_013840429.1 DESRU_RS01860 biosynthetic-type acetolactate synthase large subunit

Query= metacyc::MONOMER-18810
         (585 letters)



>NCBI__GCF_000215085.1:WP_013840429.1
          Length = 553

 Score =  580 bits (1496), Expect = e-170
 Identities = 292/562 (51%), Positives = 388/562 (69%), Gaps = 11/562 (1%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           +M GA+IL+ +L E GVE ++GYPGG  L IYD L+  +  +HILVRHEQ A HAADGYA
Sbjct: 2   KMSGAQILIDSLKEAGVETIFGYPGGQALPIYDALY-DSDLQHILVRHEQGAAHAADGYA 60

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           RA+GKVGV L TSGPG TN VTGIA AY+DS+PMV ITG VPT  +G+D+FQE D  GIT
Sbjct: 61  RASGKVGVCLATSGPGATNLVTGIANAYMDSVPMVAITGQVPTFLLGRDSFQEVDITGIT 120

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
            PI KHN++VKD++D+   +K+AF++A+TGRPGPV++DIPKD+S     YE    +++  
Sbjct: 121 LPITKHNYIVKDIKDMGRIVKEAFYVASTGRPGPVLIDIPKDISSGEMDYERNGCLNLPG 180

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           YNP  +     + +A+  +  +  P IY GGGV+ + A  EL++L+     PVT TLMGL
Sbjct: 181 YNPPREAREDLVNQALRAIAESRCPVIYAGGGVISSGAHQELKKLSETLLAPVTVTLMGL 240

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317
           G FPG     +GMLGMHG+  AN A+  CD+LIA+G RFDDRV G    F S A KIIHI
Sbjct: 241 GGFPGDHPLSLGMLGMHGSKYANYAVCECDLLIAVGVRFDDRVTGKIESFASNA-KIIHI 299

Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCL 377
           DIDP+ + K V+VDIP+ G+VK VL +L+ +++A            W E+I  W+     
Sbjct: 300 DIDPAEMGKNVQVDIPVTGDVKLVLNQLLERLEA-------RIPTAWQEKIAAWKKEYPF 352

Query: 378 KYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTM 437
            YDR+ E +KPQ ++ +I   T G A I ++VGQHQMWAAQ+Y + +PR +I+SGGLGTM
Sbjct: 353 DYDRTGETLKPQQIIREIDRQTSGQARITTEVGQHQMWAAQYYTYTKPRSFISSGGLGTM 412

Query: 438 GVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQ 497
           G G P A+G++ A PE+ V  I G+GSIQM IQEL+T + Y+ PV +  +NNGYLGMVRQ
Sbjct: 413 GYGFPAAIGVQVACPEETVFDIAGDGSIQMNIQELATAVNYELPVNVAIMNNGYLGMVRQ 472

Query: 498 WQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLDF 557
           WQE+ Y+ RYS S M + PDFVKLAE+YG  G R+ +  +V P L+ A + + + V +DF
Sbjct: 473 WQEMLYNRRYSQSEMKS-PDFVKLAESYGAEGYRITRKEEVTPVLQAAIQSR-KPVLMDF 530

Query: 558 QTDPTENVWPMVQAGKGISEML 579
             +P ENV P V  GKG++EML
Sbjct: 531 VVEPEENVLPFVPPGKGLNEML 552


Lambda     K      H
   0.319    0.135    0.407 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 906
Number of extensions: 31
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 585
Length of database: 553
Length adjustment: 36
Effective length of query: 549
Effective length of database: 517
Effective search space:   283833
Effective search space used:   283833
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)

Align candidate WP_013840429.1 DESRU_RS01860 (biosynthetic-type acetolactate synthase large subunit)
to HMM TIGR00118 (ilvB: acetolactate synthase, large subunit, biosynthetic type (EC 2.2.1.6))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00118.hmm
# target sequence database:        /tmp/gapView.770688.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00118  [M=557]
Accession:   TIGR00118
Description: acolac_lg: acetolactate synthase, large subunit, biosynthetic type
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.5e-268  877.0   0.0   2.8e-268  876.8   0.0    1.0  1  NCBI__GCF_000215085.1:WP_013840429.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000215085.1:WP_013840429.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  876.8   0.0  2.8e-268  2.8e-268       1     554 [.       3     552 ..       3     553 .] 0.99

  Alignments for each domain:
  == domain 1  score: 876.8 bits;  conditional E-value: 2.8e-268
                             TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlatsGP 73 
                                           ++ga+il++slk+ gvet+fGyPGG+ lpiydalyds+l+hilvrheq+aahaadGyarasGkvGv+latsGP
  NCBI__GCF_000215085.1:WP_013840429.1   3 MSGAQILIDSLKEAGVETIFGYPGGQALPIYDALYDSDLQHILVRHEQGAAHAADGYARASGKVGVCLATSGP 75 
                                           79*********************************************************************** PP

                             TIGR00118  74 GatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeias 146
                                           Gatnlvtgia+ay+dsvP+v++tGqv+t l+G d+fqe+di+Gitlp+tkh+++vk+ +d+ +i+keaf++as
  NCBI__GCF_000215085.1:WP_013840429.1  76 GATNLVTGIANAYMDSVPMVAITGQVPTFLLGRDSFQEVDITGITLPITKHNYIVKDIKDMGRIVKEAFYVAS 148
                                           ************************************************************************* PP

                             TIGR00118 147 tGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeasee 219
                                           tGrPGPvl+d+Pkd+++ e+++e +  ++lpgy+p  ++++  +++al +i++++ Pv+++GgGvi ++a++e
  NCBI__GCF_000215085.1:WP_013840429.1 149 TGRPGPVLIDIPKDISSGEMDYERNGCLNLPGYNPPREAREDLVNQALRAIAESRCPVIYAGGGVISSGAHQE 221
                                           ************************************************************************* PP

                             TIGR00118 220 lkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapea 292
                                           lk+l+e+l +pvt tl+GlG+fp dhpl+lgmlGmhG+k+an+av e+dlliavG+rfddrvtg++++fa++a
  NCBI__GCF_000215085.1:WP_013840429.1 222 LKKLSETLLAPVTVTLMGLGGFPGDHPLSLGMLGMHGSKYANYAVCECDLLIAVGVRFDDRVTGKIESFASNA 294
                                           ************************************************************************* PP

                             TIGR00118 293 kiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilkldeeeesikPqk 365
                                           kiihididPae+gknv+vdip+ Gd+k vl++ll++l+++  +   W eki+ wkkey++ +d++ e++kPq+
  NCBI__GCF_000215085.1:WP_013840429.1 295 KIIHIDIDPAEMGKNVQVDIPVTGDVKLVLNQLLERLEARIPTA--WQEKIAAWKKEYPFDYDRTGETLKPQQ 365
                                           *************************************9988877..*************************** PP

                             TIGR00118 366 vikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdg 438
                                           +i+e+ ++++++a +tt+vGqhqmwaaq+y+++kpr+fi+sgGlGtmG+G+Paa+G++va peetv +++Gdg
  NCBI__GCF_000215085.1:WP_013840429.1 366 IIREIDRQTSGQARITTEVGQHQMWAAQYYTYTKPRSFISSGGLGTMGYGFPAAIGVQVACPEETVFDIAGDG 438
                                           ************************************************************************* PP

                             TIGR00118 439 sfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekp 511
                                           s+qmn+qel+t+v+y++pv + i+nn +lGmv+qWqe++y++rys+++++s  pdfvklae+yG++g ri+++
  NCBI__GCF_000215085.1:WP_013840429.1 439 SIQMNIQELATAVNYELPVNVAIMNNGYLGMVRQWQEMLYNRRYSQSEMKS--PDFVKLAESYGAEGYRITRK 509
                                           **************************************************6..******************** PP

                             TIGR00118 512 eeleeklkealeskepvlldvevdkeeevlPmvapGagldelv 554
                                           ee+   l+ a++s++pvl+d++v+ ee+vlP v+pG+gl+e++
  NCBI__GCF_000215085.1:WP_013840429.1 510 EEVTPVLQAAIQSRKPVLMDFVVEPEENVLPFVPPGKGLNEML 552
                                           *****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (553 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 30.74
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory